Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study

Cerón‐Carrasco, José P.; Requena, A.; Jacquemin, Denis

doi:10.1007/s00214-012-1188-9

Cited by 25 publications

(18 citation statements)

References 125 publications

(124 reference statements)

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“…In the literature there is discussion about the functional that must be used in these types of systems 16. 49–52 The authors of refs. 50, 51 have shown that the H‐bond lengths are overestimated from the B3LYP functional, but those of ref.…”

Section: Methodsmentioning

confidence: 99%

Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Villani¹

2013

ChemPhysChem

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Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.

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Section: Methodsmentioning

confidence: 99%

Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Villani¹

2013

ChemPhysChem

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“…The subtractive nature of the ONIOM method means that undefined terms in the MM expression do not contribute to the overall energy if the relevant atoms are entirely within the QM region, making it ideally suited for the purposes of the current study. We note that this approach has been widely adopted for QM/MM studies of DNA and related structures 30– 32 . Pure molecular mechanics (MM) geometry optimisation was also performed using the GROMACS simulation package 33 and the AMBERParmbsc0 force field 34 , including RESP charges derived for modified bases in our previous work 19 , in explicit aqueous phase, specifically TIP3P water 35 with Na + and Cl - counter ions to create a neutral system.…”

Section: Computational Methodologymentioning

confidence: 99%

Theoretical modelling of epigenetically modified DNA sequences

et al. 2015

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We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

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“…[12][13][14][15][16] 碱基对内质子转移反应受到多种环境因素的影响, 水溶剂、碱基序列、堆积效应和各种离子等都会影响碱基对内质子转移. 因此科学家开始关注这些环境因素的作用, [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32] 目前的研究结果表明, 水分子有助于碱基对阴离子发生单质子转移反应, 17,18 不同碱基排序对碱基对阴离子的单质子转移分别起到促进和阻碍作用, 19 堆积效应在质子转移过程中改变氢键键长并保持碱基对的平面性, 20 一些金属离子也有助于单质子转移反应的发生. 32 Table 2 Charge…”

Section: 引言unclassified

Double-Proton-Transfer Reaction in Guanine-Cytosine Base Pair Embedded in B-Form DNA

Yue-Xia¹,

Wang

Si-Min³

et al. 2013

Acta Physico-Chimica Sinica

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The double-proton-transfer reaction of the isolated guanine-cytosine (GC) base pair and four DNA trimers with different nucleobase sequences (dATGCAT, dGCGCGC, dTAGCTA, and dCGGCCG) are studied by quantum mechanical calculations using ONIOM(M06-2X/6-31G*:PM3). Proton-transfer patterns, energy and structural properties are analyzed to gain insight into the double-proton-transfer mechanism with consideration to environmental factors. In the gas phase, a stepwise mechanism is found for the dCGGCCG trimer, and a concerted mechanism is found in the other four models. The computational results demonstrate that electrostatic interaction of the peripheral and middle base pairs have a pronounced effect on double-proton-transfer pattern of GC base pairs. The structures with dATGCAT and dGCGCGC sequences facilitate H4a proton transfer and those with dTAGCTA and dCGGCCG sequence facilitate H1 proton transfer. The high proton affinity of cytosine at N3 facilitates H1 proton transfer. In aqueous solution, electrostatic interactions are reduced and the products of single-proton-transfer in the stepwise mechanism are stabilized. This results in a stepwise transfer pattern becoming favorable. Solvent effects favor the single-proton-transfer reaction more than gas phase conditions, but increase the reaction energy of double-proton-transfer.

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Impact of DFT functionals on the predicted magnesium–DNA interaction: an ONIOM study

Cited by 25 publications

References 125 publications

Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

Theoretical modelling of epigenetically modified DNA sequences

Double-Proton-Transfer Reaction in Guanine-Cytosine Base Pair Embedded in B-Form DNA

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